SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
Finding chimeric contigs in metagenome kumara Bioinformatics 0 10-16-2014 01:54 PM
finding novel proteins from denovo assembly bioman1 Bioinformatics 0 03-13-2014 07:11 AM
Finding contig repeat counts by mapping contigs to the reference genome misagh Bioinformatics 1 01-09-2014 05:41 AM
Finding SMALL peptides in de novo assembly gege_55 Bioinformatics 3 03-07-2013 01:06 AM
Finding a specific gene in transcriptome assembly psurana Bioinformatics 4 09-22-2011 01:14 PM

Reply
 
Thread Tools
Old 11-24-2014, 03:59 AM   #1
mandar.bobade60
Member
 
Location: India

Join Date: Jun 2013
Posts: 14
Default Finding contaminant contigs in assembly

Hi,

I have generated plant mitochondrial assembly for which I would like to find contamination from chloroplast as well as nuclear genome. I have also run BlastN using same species nuclear genome and chloroplast genome database, and now with results I have some alignments with multiple scaffolds generated.

My question is, if it is wise cutting down sequences from assembly which are having high identity with substantive e-value with subject sequences or I need to see some other criteria along with identity and e-value?

Any help would be highly appreciated...
mandar.bobade60 is offline   Reply With Quote
Old 12-04-2014, 03:31 AM   #2
bastianwur
Member
 
Location: Germany/Netherlands

Join Date: Feb 2014
Posts: 98
Default

What about the length?
Longer alignment > smaller one.
bastianwur is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 09:45 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO